Special Collection

Liquid tumor sample must contain a minimum of 20% disease content for SNV, 60% disease content for CNV

Tumor sample must contain a minimum of 20% tumor for SNV, 60% tumor for CNV

Outpatient Submit with Specimen

Oncology Genetic Requisition

For samples collected in the state of New York, please use: New York State Oncology Genetic Test Requisition Form and Consent

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)4 mLAlternate
Buccal swabBuccal swab kit4 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)4 mLPreferred
Germline: SalivaOragene saliva collection tube2 tubesAlternate
Germline: Buccal swabBuccal swab kit4 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Outpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

Unacceptable Conditions

Wrong type of specimen, Inadequate tissue, Clotted specimen, Insufficient tumor content in tumor sample, Wrong collection tube, FFPE specimens processed using strong acid decalcification are not acceptable; EDTA and Formical are accepted. 

Stability

Unstained slides: Room temperature 12 months

Paraffin embedded tissue: Room temperature 12 months

Tissue (Snap-frozen): Frozen 36 months

OCT-embedded tissue: Frozen 36 months

Tissue (Fresh): Refrigerated 3 days
Tissue (Fresh): Room temperature 4 hours

Bone marrow: Room temperature 3 days
Bone marrow: Refrigerated 7 days

Tissue scrolls (FFPE): Room temperature 12 months

Whole blood: Room temperature 3 days
Whole blood: Refrigerated 7 days

Buccal swab: Room temperature 7 days
Buccal swab: Refrigerated 7 days

Remarks

This test requires submission of both a disease-involved sample (somatic sample) and non-disease-involved sample (germline comparator sample) from the patient. For malignant conditions, the disease-involved sample must contain a minimum of 20% tumor or disease content for single-nucleotide and small insertion-deletion variant resolution, and 60% tumor or disease content for sensitive resolution of copy number variation (CNV) and loss of heterozygosity (LOH) to enable interpretation and reporting. Sensitivity in calling CNV and LOH will be limited, and at times, assay resolution of these events will preclude interpretation and reporting of CNV and LOH, if the submitted specimen contains less than 60% disease-content. 

If submitting a tissue scroll or slide specimen, please submit 10-15 FFPE scrolls or slides (5-10 microns thick) and an adjacent H&E slide, or use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory (approximately 300mm2 at 10 microns thickness).

For questions, please call the NCH Institute for Genomic Medicine (IGM) Clinical Laboratory at (614) 722-5321 and ask to speak with a laboratory genetic counselor.

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Lab Area

Institute for Genomic Medicine

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

Special Collection

Liquid tumor sample must contain a minimum of 20% disease content for SNV, 60% disease content for CNV

Tumor sample must contain a minimum of 20% tumor for SNV, 60% tumor for CNV

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)4 mLAlternate
Buccal swabBuccal swab kit4 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)4 mLPreferred
Germline: SalivaOragene saliva collection tube2 tubesAlternate
Germline: Buccal swabBuccal swab kit4 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette30 mgAlternate
Tissue (Snap-frozen)Cryogenic tube30 mgAlternate
OCT-embedded tissueTissue cassette30 mgAlternate
OCT-embedded tissueCryogenic tube30 mgAlternate
Tissue (Fresh)Tissue culture transport media30 mgAlternate
Tissue (Fresh)Sterile container with saline30 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)1 mLAlternate
Buccal swabBuccal swab kit2 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)1 mLPreferred
Germline: SalivaOragene saliva collection tube1 tubesAlternate
Germline: Buccal swabBuccal swab kit2 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Inpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

Unacceptable Conditions

Wrong type of specimen, Inadequate tissue, Clotted specimen, Insufficient tumor content in tumor sample, Wrong collection tube, FFPE specimens processed using strong acid decalcification are not acceptable; EDTA and Formical are accepted. 

Stability

Unstained slides: Room temperature 12 months

Paraffin embedded tissue: Room temperature 12 months

Tissue (Snap-frozen): Frozen 36 months

OCT-embedded tissue: Frozen 36 months

Tissue (Fresh): Refrigerated 3 days
Tissue (Fresh): Room temperature 4 hours

Bone marrow: Room temperature 3 days
Bone marrow: Refrigerated 7 days

Tissue scrolls (FFPE): Room temperature 12 months

Whole blood: Room temperature 3 days
Whole blood: Refrigerated 7 days

Buccal swab: Room temperature 7 days
Buccal swab: Refrigerated 7 days

Remarks

This test requires submission of both a disease-involved sample (somatic sample) and non-disease-involved sample (germline comparator sample) from the patient. For malignant conditions, the disease-involved sample must contain a minimum of 20% tumor or disease content for single-nucleotide and small insertion-deletion variant resolution, and 60% tumor or disease content for sensitive resolution of copy number variation (CNV) and loss of heterozygosity (LOH) to enable interpretation and reporting. Sensitivity in calling CNV and LOH will be limited, and at times, assay resolution of these events will preclude interpretation and reporting of CNV and LOH, if the submitted specimen contains less than 60% disease-content. 

If submitting a tissue scroll or slide specimen, please submit 10-15 FFPE scrolls or slides (5-10 microns thick) and an adjacent H&E slide, or use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory (approximately 300mm2 at 10 microns thickness).

For questions, please call the NCH Institute for Genomic Medicine (IGM) Clinical Laboratory at (614) 722-5321 and ask to speak with a laboratory genetic counselor.

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Lab Area

Institute for Genomic Medicine

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

Estimated Patient Price

> $5000

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Methodology

Next Generation Sequencing (NGS)

Special Collection

Liquid tumor sample must contain a minimum of 20% disease content for SNV, 60% disease content for CNV

Tumor sample must contain a minimum of 20% tumor for SNV, 60% tumor for CNV

Outpatient Submit with Specimen

Oncology Genetic Requisition

For samples collected in the state of New York, please use: New York State Oncology Genetic Test Requisition Form and Consent

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)4 mLAlternate
Buccal swabBuccal swab kit4 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)4 mLPreferred
Germline: SalivaOragene saliva collection tube2 tubesAlternate
Germline: Buccal swabBuccal swab kit4 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette30 mgAlternate
Tissue (Snap-frozen)Cryogenic tube30 mgAlternate
OCT-embedded tissueTissue cassette30 mgAlternate
OCT-embedded tissueCryogenic tube30 mgAlternate
Tissue (Fresh)Tissue culture transport media30 mgAlternate
Tissue (Fresh)Sterile container with saline30 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)1 mLAlternate
Buccal swabBuccal swab kit2 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)1 mLPreferred
Germline: SalivaOragene saliva collection tube1 tubesAlternate
Germline: Buccal swabBuccal swab kit2 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Inpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

Outpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

InLab Processing

Send to the Institute for Genomic Medicine Lab with all submitted paperwork. CPA needs to order GENSP in Sunquest for Non-EPIC lab order. For Saliva sample and Buccal Swab sample, families can collect sample at home and can mail in the sample and lab order to CPA or drop off the sample with a copy of the lab order at an NCH lab location to be forwarded to CPA.

Stability

Unstained slides: Room temperature 12 months

Paraffin embedded tissue: Room temperature 12 months

Tissue (Snap-frozen): Frozen 36 months

OCT-embedded tissue: Frozen 36 months

Tissue (Fresh): Refrigerated 3 days
Tissue (Fresh): Room temperature 4 hours

Bone marrow: Room temperature 3 days
Bone marrow: Refrigerated 7 days

Tissue scrolls (FFPE): Room temperature 12 months

Whole blood: Room temperature 3 days
Whole blood: Refrigerated 7 days

Buccal swab: Room temperature 7 days
Buccal swab: Refrigerated 7 days

Unacceptable Conditions

Wrong type of specimen, Inadequate tissue, Clotted specimen, Insufficient tumor content in tumor sample, Wrong collection tube, FFPE specimens processed using strong acid decalcification are not acceptable; EDTA and Formical are accepted. 

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Remarks

This test requires submission of both a disease-involved sample (somatic sample) and non-disease-involved sample (germline comparator sample) from the patient. For malignant conditions, the disease-involved sample must contain a minimum of 20% tumor or disease content for single-nucleotide and small insertion-deletion variant resolution, and 60% tumor or disease content for sensitive resolution of copy number variation (CNV) and loss of heterozygosity (LOH) to enable interpretation and reporting. Sensitivity in calling CNV and LOH will be limited, and at times, assay resolution of these events will preclude interpretation and reporting of CNV and LOH, if the submitted specimen contains less than 60% disease-content. 

If submitting a tissue scroll or slide specimen, please submit 10-15 FFPE scrolls or slides (5-10 microns thick) and an adjacent H&E slide, or use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory (approximately 300mm2 at 10 microns thickness).

For questions, please call the NCH Institute for Genomic Medicine (IGM) Clinical Laboratory at (614) 722-5321 and ask to speak with a laboratory genetic counselor.

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Estimated Patient Price

> $5000

DC Code

5321

Downtime Availability

4-Not available
Outpatient Requirements

Special Collection

Liquid tumor sample must contain a minimum of 20% disease content for SNV, 60% disease content for CNV

Tumor sample must contain a minimum of 20% tumor for SNV, 60% tumor for CNV

Outpatient Submit with Specimen

Oncology Genetic Requisition

For samples collected in the state of New York, please use: New York State Oncology Genetic Test Requisition Form and Consent

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)4 mLAlternate
Buccal swabBuccal swab kit4 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)4 mLPreferred
Germline: SalivaOragene saliva collection tube2 tubesAlternate
Germline: Buccal swabBuccal swab kit4 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Outpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

Unacceptable Conditions

Wrong type of specimen, Inadequate tissue, Clotted specimen, Insufficient tumor content in tumor sample, Wrong collection tube, FFPE specimens processed using strong acid decalcification are not acceptable; EDTA and Formical are accepted. 

Stability

Unstained slides: Room temperature 12 months

Paraffin embedded tissue: Room temperature 12 months

Tissue (Snap-frozen): Frozen 36 months

OCT-embedded tissue: Frozen 36 months

Tissue (Fresh): Refrigerated 3 days
Tissue (Fresh): Room temperature 4 hours

Bone marrow: Room temperature 3 days
Bone marrow: Refrigerated 7 days

Tissue scrolls (FFPE): Room temperature 12 months

Whole blood: Room temperature 3 days
Whole blood: Refrigerated 7 days

Buccal swab: Room temperature 7 days
Buccal swab: Refrigerated 7 days

Remarks

This test requires submission of both a disease-involved sample (somatic sample) and non-disease-involved sample (germline comparator sample) from the patient. For malignant conditions, the disease-involved sample must contain a minimum of 20% tumor or disease content for single-nucleotide and small insertion-deletion variant resolution, and 60% tumor or disease content for sensitive resolution of copy number variation (CNV) and loss of heterozygosity (LOH) to enable interpretation and reporting. Sensitivity in calling CNV and LOH will be limited, and at times, assay resolution of these events will preclude interpretation and reporting of CNV and LOH, if the submitted specimen contains less than 60% disease-content. 

If submitting a tissue scroll or slide specimen, please submit 10-15 FFPE scrolls or slides (5-10 microns thick) and an adjacent H&E slide, or use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory (approximately 300mm2 at 10 microns thickness).

For questions, please call the NCH Institute for Genomic Medicine (IGM) Clinical Laboratory at (614) 722-5321 and ask to speak with a laboratory genetic counselor.

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Lab Area

Institute for Genomic Medicine

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome
Inpatient Requirements

Special Collection

Liquid tumor sample must contain a minimum of 20% disease content for SNV, 60% disease content for CNV

Tumor sample must contain a minimum of 20% tumor for SNV, 60% tumor for CNV

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)4 mLAlternate
Buccal swabBuccal swab kit4 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)4 mLPreferred
Germline: SalivaOragene saliva collection tube2 tubesAlternate
Germline: Buccal swabBuccal swab kit4 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette30 mgAlternate
Tissue (Snap-frozen)Cryogenic tube30 mgAlternate
OCT-embedded tissueTissue cassette30 mgAlternate
OCT-embedded tissueCryogenic tube30 mgAlternate
Tissue (Fresh)Tissue culture transport media30 mgAlternate
Tissue (Fresh)Sterile container with saline30 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)1 mLAlternate
Buccal swabBuccal swab kit2 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)1 mLPreferred
Germline: SalivaOragene saliva collection tube1 tubesAlternate
Germline: Buccal swabBuccal swab kit2 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Inpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

Unacceptable Conditions

Wrong type of specimen, Inadequate tissue, Clotted specimen, Insufficient tumor content in tumor sample, Wrong collection tube, FFPE specimens processed using strong acid decalcification are not acceptable; EDTA and Formical are accepted. 

Stability

Unstained slides: Room temperature 12 months

Paraffin embedded tissue: Room temperature 12 months

Tissue (Snap-frozen): Frozen 36 months

OCT-embedded tissue: Frozen 36 months

Tissue (Fresh): Refrigerated 3 days
Tissue (Fresh): Room temperature 4 hours

Bone marrow: Room temperature 3 days
Bone marrow: Refrigerated 7 days

Tissue scrolls (FFPE): Room temperature 12 months

Whole blood: Room temperature 3 days
Whole blood: Refrigerated 7 days

Buccal swab: Room temperature 7 days
Buccal swab: Refrigerated 7 days

Remarks

This test requires submission of both a disease-involved sample (somatic sample) and non-disease-involved sample (germline comparator sample) from the patient. For malignant conditions, the disease-involved sample must contain a minimum of 20% tumor or disease content for single-nucleotide and small insertion-deletion variant resolution, and 60% tumor or disease content for sensitive resolution of copy number variation (CNV) and loss of heterozygosity (LOH) to enable interpretation and reporting. Sensitivity in calling CNV and LOH will be limited, and at times, assay resolution of these events will preclude interpretation and reporting of CNV and LOH, if the submitted specimen contains less than 60% disease-content. 

If submitting a tissue scroll or slide specimen, please submit 10-15 FFPE scrolls or slides (5-10 microns thick) and an adjacent H&E slide, or use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory (approximately 300mm2 at 10 microns thickness).

For questions, please call the NCH Institute for Genomic Medicine (IGM) Clinical Laboratory at (614) 722-5321 and ask to speak with a laboratory genetic counselor.

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Lab Area

Institute for Genomic Medicine

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

Estimated Patient Price

> $5000
Overview/Billing

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).
Interpretation

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Methodology

Next Generation Sequencing (NGS)
NCH Lab Only

Special Collection

Liquid tumor sample must contain a minimum of 20% disease content for SNV, 60% disease content for CNV

Tumor sample must contain a minimum of 20% tumor for SNV, 60% tumor for CNV

Outpatient Submit with Specimen

Oncology Genetic Requisition

For samples collected in the state of New York, please use: New York State Oncology Genetic Test Requisition Form and Consent

Collect

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette50 mgAlternate
Tissue (Snap-frozen)Cryogenic tube50 mgAlternate
OCT-embedded tissueTissue cassette50 mgAlternate
OCT-embedded tissueCryogenic tube50 mgAlternate
Tissue (Fresh)Tissue culture transport media50 mgAlternate
Tissue (Fresh)Sterile container with saline50 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)4 mLAlternate
Buccal swabBuccal swab kit4 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)4 mLPreferred
Germline: SalivaOragene saliva collection tube2 tubesAlternate
Germline: Buccal swabBuccal swab kit4 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Minimum Volume

Specimen TypeType of ContainerVolume of SpecimenStatus
Unstained tissue slidesUnstained slides and consecutive cut H&E10 slides,
10 microns thick		Preferred
Paraffin embedded tissueParaffin block1 blockPreferred
Tissue (Snap-frozen)Tissue cassette30 mgAlternate
Tissue (Snap-frozen)Cryogenic tube30 mgAlternate
OCT-embedded tissueTissue cassette30 mgAlternate
OCT-embedded tissueCryogenic tube30 mgAlternate
Tissue (Fresh)Tissue culture transport media30 mgAlternate
Tissue (Fresh)Sterile container with saline30 mgAlternate
Bone marrow4 mL Purple tube (EDTA)4 mLAlternate
Tissue scrolls (FFPE)Sterile container10-15 scrolls,
5-10 microns thick		Alternate
Whole blood4 mL Purple tube (EDTA)1 mLAlternate
Buccal swabBuccal swab kit2 swabsAlternate
    
Germline: Whole blood4 mL Purple tube (EDTA)1 mLPreferred
Germline: SalivaOragene saliva collection tube1 tubesAlternate
Germline: Buccal swabBuccal swab kit2 swabsAlternate
DNA
*Must be extracted in a
CLIA approved lab		Microcentrifuge tubeContact IGM labAlternate

Inpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

Outpatient Specimen Preparation

Unstained slides: Keep at room temperature
                          Protect from heat
                          Must accompany H&E slide from adjacent section
                          Samples decalcified with a strong acid are not accepted. EDTA-based decalcification                                      methods (such as Formical) are acceptable.
                        
Paraffin embedded tissue: Keep at room temperature
                                       Protect from heat

Tissue (Snap-frozen): Freeze immediately after collection
                                 Transport to laboratory as soon as possible

OCT-embedded tissue: Freeze immediately after collection
                                  Transport to laboratory as soon as possible

Tissue (Fresh): Do not add fixative
                         Do not formalin fix the sample
                         Transport to laboratory as soon as possible
                         Keep at room temperature or refrigerate

Bone marrow: Do not add fixative
                     Transport to laboratory as soon as possible
                      Keep at room temperature or refrigerate

Whole blood: Keep at room temperature or refrigerate 
                      
Buccal swab: Keep at room temperature or refrigerate

Tissue scrolls: Must accompany H&E slide from adjacent section
                     Protect from heat, Keep at room temperature

Saliva: Keep at room temperature

InLab Processing

Send to the Institute for Genomic Medicine Lab with all submitted paperwork. CPA needs to order GENSP in Sunquest for Non-EPIC lab order. For Saliva sample and Buccal Swab sample, families can collect sample at home and can mail in the sample and lab order to CPA or drop off the sample with a copy of the lab order at an NCH lab location to be forwarded to CPA.

Stability

Unstained slides: Room temperature 12 months

Paraffin embedded tissue: Room temperature 12 months

Tissue (Snap-frozen): Frozen 36 months

OCT-embedded tissue: Frozen 36 months

Tissue (Fresh): Refrigerated 3 days
Tissue (Fresh): Room temperature 4 hours

Bone marrow: Room temperature 3 days
Bone marrow: Refrigerated 7 days

Tissue scrolls (FFPE): Room temperature 12 months

Whole blood: Room temperature 3 days
Whole blood: Refrigerated 7 days

Buccal swab: Room temperature 7 days
Buccal swab: Refrigerated 7 days

Unacceptable Conditions

Wrong type of specimen, Inadequate tissue, Clotted specimen, Insufficient tumor content in tumor sample, Wrong collection tube, FFPE specimens processed using strong acid decalcification are not acceptable; EDTA and Formical are accepted. 

Days Performed

Monday through Saturday

Set Up Schedule

All tests not performed daily.

Typical Turnaround

3 weeks

Remarks

This test requires submission of both a disease-involved sample (somatic sample) and non-disease-involved sample (germline comparator sample) from the patient. For malignant conditions, the disease-involved sample must contain a minimum of 20% tumor or disease content for single-nucleotide and small insertion-deletion variant resolution, and 60% tumor or disease content for sensitive resolution of copy number variation (CNV) and loss of heterozygosity (LOH) to enable interpretation and reporting. Sensitivity in calling CNV and LOH will be limited, and at times, assay resolution of these events will preclude interpretation and reporting of CNV and LOH, if the submitted specimen contains less than 60% disease-content. 

If submitting a tissue scroll or slide specimen, please submit 10-15 FFPE scrolls or slides (5-10 microns thick) and an adjacent H&E slide, or use this Tissue Scroll Calculator tool to determine the thickness and number of tissue scrolls to send to the laboratory (approximately 300mm2 at 10 microns thickness).

For questions, please call the NCH Institute for Genomic Medicine (IGM) Clinical Laboratory at (614) 722-5321 and ask to speak with a laboratory genetic counselor.

Clinical Information

This test is intended for a patient with known or suspected cancer, hematologic disease, or somatic disorders (e.g. somatic overgrowth, vascular malformation, or other mosaic disease). Genomic characterization of a tumor or disease-involved tissue can aid in diagnosis, prognosis, and medical management, such as making treatment decisions and evaluating eligibility for targeted therapies and clinical trials. This test can also identify germline disease predisposition. 

This test consists of paired exome sequencing analysis on both disease-involved and non-disease involved samples.  See attached list of germline and somatic genes reviewed during interpretation. In total, CNV, LOH, Tumor mutational burden (TMB) and small variants/indels will be reported if identified.

The presence of pathogenic variant(s) confined to disease-involved tissue(s) can be found in malignancies/somatic diseases, and these variants are described as somatic in origin. Sometimes, a pathogenic variant is also detected in the patient’s germline sample, which indicates that the variant is germline in origin and occurs throughout all cells in the body.  Germline variants can be associated with hereditary predisposition to disease.

This test also reports tumor mutational burden (TMB). The TMB value serves as a biomarker in consideration of the potential applicability of therapies targeting immune checkpoint inhibition. TMB values of greater than or equal to 10 are described as TMB high, values less than or equal to 5 are described as TMB low, and values between those ranges are defined as TMB intermediate. Tumors with a high TMB can generate neoantigens, representing abnormal proteins, that can trigger an immune response.  For this reason, TMB-high tumors may be more likely to respond to immunotherapy. TMB is used to inform the cancer patient population who would be more likely to benefit from immune checkpoint inhibitors.

In the setting of high-TMB (defined in this context as 10 mutations/Mb) the FDA has approved pembrolizumab for adult and pediatric patients with advanced-stage solid tumors following disease progression on standard-of-care therapy who lack an alternative treatment option.  Dozens of other immunotherapies have been approved in various cancer contexts. Ability to report TMB may be tumor specimen dependent. Please contact the laboratory for further information.

Synonyms

  • Tumor Normal Exome, Tumor Normal WES, Tumor-Normal Exome, Tumor-Normal WES, Somatic Germline Paired Exome, Somatic Germline Paired WES, Tumor Normal Paired Exome, Tumor-Normal Paired Exome, Exome Sequencing, Cancer Exome, Oncology Exome, Tumor Exome, Somatic Exome, IGM Test, Comparator Exome

Methodology

Next Generation Sequencing (NGS)

CPT Codes

81415, 81416 used for new germline and new somatic sample.
81417, 81416 used for previous germline sample already analyzed by SDGC testing, and a new somatic sample (such as a relapse).

Estimated Patient Price

> $5000

DC Code

5321

Downtime Availability

4-Not available

Lab Area

Lab Area
Institute for Genomic Medicine

New York DOH Approval Status

New York DOH Approval Status
This test is New York state approved

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